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Managing Chicken Coccidiosis in Small Flocks During Summer

Coccidiosis can be a challenge for small flocks, especially those choosing antibiotic-free production. This article provides information on the parasite's life cycle, clinical signs, and treatment.

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Updated:

January 20, 2026

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Coccidiosis is caused by protozoan parasites from the genus Eimeria. These parasites are host-specific, and many species occupy a specific segment of the intestinal tract. Coccidiosis may be one of the most common diseases affecting small flocks worldwide, causing decreased production or performance and even mortality. This disease can be complicated by bacterial agents such as Clostridium perfringens. Vaccination, preventative medication, and good management practices can help control the disease.

Coccidiosis is especially prevalent in high-density flocks and in flocks where animals have direct contact with their feces. Virtually every poultry flock raised on litter is affected by coccidiosis to some degree. Birds love to peck the floor, and in doing so, they ingest the oocytes (parasite eggs) that are present in the manure of infected birds. Birds in backyard flocks are often not provided with enough bedding material in the coop. The more contact the animals have with fecal material, the greater their risk of developing serious coccidiosis.

Following ingestion, the parasite undergoes its complex life cycle within the intestinal tract, during which it replicates and ruptures the intestinal cells. The infected animal then sheds oocysts in the feces. After a few intestinal cycles of the parasite, birds can develop long-lasting protective immunity, but this immunity is specific to the particular species of coccidia. Challenge with a different species will lead to infection and disease, depending on the number of oocysts consumed.

Animals raised in cages with no contact with fecal material do not develop the disease. However, it is important to note that if caged animals have access to manure (due to poor design or inadequate cage maintenance), the disease will develop.

Clinical Signs

Under heavy infections, birds may appear depressed with ruffled feathers. Diarrhea and dehydration may be present. Blood (Figure 1) and/or clear to bright orange mucus (Figures 2 and 3, respectively) may be present in the feces. The skin of affected birds may appear paler than unaffected birds. Body weight and feed conversion may also be affected in heavy infections with more pathogenic strains of coccidia.

Figure 1. Fecal material with fresh blood. Photo credit: Dr. Lorenzoni

Fecal matter mixed with mucus — Figure 2. Fecal matter mixed with abundant clear intestinal mucus. Photo credit: Dr. Lorenzoni.

Orange mucus inside the mid-section of the small intestine — Figure 3. Abundant orange mucus inside the mid-section of the small intestine of a broiler chicken. This orange material can be found mixed with fecal matter. Photo credit: Dr. Lorenzoni.

Diagnosis

Fecal material can be taken to an animal diagnostic laboratory. Oocysts are easily visible under a light microscope. If there are dead animals, they can also be taken to the laboratory for examination. An experienced poultry veterinarian can usually diagnose coccidiosis upon visual inspection of the intestines.

Control

One of the easiest ways to control coccidiosis is to purchase vaccinated birds. Vaccines are given at the hatchery on the day of hatch. Once the animals have developed immunity, they will be resistant to the strains of coccidia used in the vaccine they received.

Most backyard chickens are not vaccinated. In this case, the disease can be managed by controlling exposure to the parasite, which may reside in manure. Fortunately, a reduction in parasite load is normally all it takes to control coccidia in your birds. Ingesting a few parasites is not a problem and actually helps birds develop strong immunity to them. The key is to prevent birds from consuming large numbers of parasites at once, as this can cause clinical disease or a level of disease that produces noticeable symptoms.

This can be achieved with good management practices. Bird density and litter quality are crucial factors in determining parasite load in the chicken coop. Ideal bird density depends on the type of chicken you are raising and on your particular circumstances and setup. As a rule of thumb, density is on target as long as the litter (bedding material) is kept in good condition (dry and fluffy). If the litter deteriorates too rapidly, you probably have a poor setup that does not support your current bird density. A low bird density (>5 ft² per bird) is preferred in non-vaccinated animals to minimize parasite buildup in the litter. Do your best to keep your birds on a thick, dry layer of litter. This will effectively dilute the fecal material, reducing the number of coccidia ingested during litter pecking.

Wet litter usually cakes. Caked litter will keep fecal matter undiluted and in direct contact with the animals. Every time birds peck caked litter, chances are they are likely to consume higher numbers of parasites. Two places where litter needs to be monitored frequently are around the feeders and around the waterers. Birds tend to spend longer amounts of time in these areas, thus the volume of their fecal matter is higher there. During the summer, this problem can be challenging because birds will consume more water. More water will be spilled near the waterers, and fecal matter will have a high moisture content. In a small coop, one option is to move the feeders and waterers to a dry spot every day or so. Another strategy, more common in medium to large-sized operations, is to remove wet or caked litter material and replenish it with fresh material regularly.

Treatment

Treatment should be reserved for sick animals. Medicating birds at the wrong time (too early or too often) will interfere with the development of protective immunity. Do not use medicated feed during the first 14 days of life. If birds appear to be sick with coccidiosis after day 14, the best course of action is to consult with a local veterinarian and to conduct a fecal flotation analysis. Alternatively, you can replace the regular starter feed with medicated feed. Medicated feed containing amprolium is commercially available and can be purchased without a veterinary prescription. Read the label on the feed bag and make sure that the feed contains amprolium. Some of the "medicated" feeds contain products other than amprolium that are not intended to treat coccidiosis (like probiotics).

On hot days, birds tend to limit their feed consumption. For this reason, it is important that the animals receive only medicated feed. Any other feed supplementation will decrease the effective dose of amprolium.